I've had something similar happen. Had a gentleman, who I assume is Islamic*, hold up the flight from taking off as he was praying. He'd gone to the back of the plane near the air-waitresses and the shiatters, put his jacket down, and was doing the up and down thing. Head air-waitress kept making an announcement for everyone to get in their seats. He kept praying.

Mildly annoying, but we got wheels up in a reasonable time. I can certainly respect (but not agree with) people who want to pray. However, what I can't accept is when you do it in such a way as to interfere with 100+ other people. It's not like prayer-time magically moved around. You knew when you'd have to go through your ritual. Plan accordingly and don't inconvenience the rest of us.

On one flight I was on across the Atlantic, the Orthodox Jewish man who was sitting beside me got up and went to an emergency exit to pray. It involved bowing his head at the door and touching the handle for some reason. A very nice flight attendant suggested to him that maybe just maybe he was making the other passengers a little bit nervous. He came out of a trance, apologized, and sat down again. I thought that was a great way to handle it.